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Chaudhary S, Selvaraj V, Awasthi P, Bhuria S, Purohit R, Kumar S, Hallan V. Small Heat Shock Protein (sHsp22.98) from Trialeurodes vaporariorum Plays Important Role in Apple Scar Skin Viroid Transmission. Viruses 2023; 15:2069. [PMID: 37896846 PMCID: PMC10611230 DOI: 10.3390/v15102069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/11/2023] [Accepted: 09/16/2023] [Indexed: 10/29/2023] Open
Abstract
Trialeurodes vaporariorum, commonly known as the greenhouse whitefly, severely infests important crops and serves as a vector for apple scar skin viroid (ASSVd). This vector-mediated transmission may cause the spread of infection to other herbaceous crops. For effective management of ASSVd, it is important to explore the whitefly's proteins, which interact with ASSVd RNA and are thereby involved in its transmission. In this study, it was found that a small heat shock protein (sHsp) from T. vaporariorum, which is expressed under stress, binds to ASSVd RNA. The sHsp gene is 606 bp in length and encodes for 202 amino acids, with a molecular weight of 22.98 kDa and an isoelectric point of 8.95. Intermolecular interaction was confirmed through in silico analysis, using electrophoretic mobility shift assays (EMSAs) and northwestern assays. The sHsp22.98 protein was found to exist in both monomeric and dimeric forms, and both forms showed strong binding to ASSVd RNA. To investigate the role of sHsp22.98 during ASSVd infection, transient silencing of sHsp22.98 was conducted, using a tobacco rattle virus (TRV)-based virus-induced gene silencing system. The sHsp22.98-silenced whiteflies showed an approximate 50% decrease in ASSVd transmission. These results suggest that sHsp22.98 from T. vaporariorum is associated with viroid RNA and plays a significant role in transmission.
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Affiliation(s)
- Savita Chaudhary
- Plant Virology Laboratory, Division of Biotechnology, CSIR—Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India (R.P.)
| | - Vijayanandraj Selvaraj
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India (R.P.)
- Plant Molecular Virology Laboratory, Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow 226001, Uttar Pradesh, India
| | - Preshika Awasthi
- Plant Virology Laboratory, Division of Biotechnology, CSIR—Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Swati Bhuria
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India (R.P.)
- Plant Molecular Virology Laboratory, Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow 226001, Uttar Pradesh, India
| | - Rituraj Purohit
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India (R.P.)
- Bioinformatics Lab, Division of Biotechnology, CSIR—Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Surender Kumar
- Plant Virology Laboratory, Division of Biotechnology, CSIR—Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Vipin Hallan
- Plant Virology Laboratory, Division of Biotechnology, CSIR—Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India (R.P.)
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Dhir S, Mathioudakis MM, Hasiów-Jaroszewska B, Hallan V. Serological and molecular analysis indicates the presence of distinct viral genotypes of Apple stem pitting virus in India. 3 Biotech 2021; 11:278. [PMID: 34040927 DOI: 10.1007/s13205-021-02798-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/15/2021] [Indexed: 01/10/2023] Open
Abstract
Recombination leads to the generation of new viral progeny which remain undetected by routine testing procedures and may be a threat to the infected host. Here, we have characterised the complete genome sequences of two isolates of Apple stem pitting virus from apple cv. Red Chief (Palampur) and cv. Gold Spur (N) with distinct serological reactivities. The viral genomes consisted of 9267 nucleotides for isolate Palampur and 9254 nucleotides for isolate N, excluding the poly (A) tail and contained 5five open reading frames (ORFs). Isolate N shared 80.8% sequence identity with ASPV apple isolate GA2 from China, while isolate Palampur shared 81.4% sequence identity with ASPV apple isolate PB66 from the United Kingdom. The serological difference of isolates N and Palampur along with their low sequence identity indicated the existence of two distinct virus genotypes which was corroborated by evolutionary and genetic differentiation analyses. Recombination events were detected in the RdRp and CP sequences of Palampur isolate thereby suggesting the role of recombination in the evolution of distinct virus genotypes. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02798-5.
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Affiliation(s)
- Sunny Dhir
- Plant Virus Lab, Council of Scientific & Industrial Research, Institute of Himalayan Bioresource Technology, Palampur, HP 176061 India
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, Uttar Pradesh 201313 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Matthaios M Mathioudakis
- Plant Pathology Laboratory, Institute of Olive Tree, Subtropical Crops and Viticulture, ELGO-DIMITRA, Karamanlis Ave. 167, 73134 Chania, Greece
| | - Beata Hasiów-Jaroszewska
- Department of Virology and Bacteriology, Institute of Plant Protection-National Research Institute, ul. Wł. Węgorka 20, 60-318 Poznan, Poland
| | - Vipin Hallan
- Plant Virus Lab, Council of Scientific & Industrial Research, Institute of Himalayan Bioresource Technology, Palampur, HP 176061 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
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Noorani MS, Khan JA. Development of a novel polyprobe for simultaneous detection of six viruses infecting stone and pome fruits. 3 Biotech 2020; 10:389. [PMID: 32832339 DOI: 10.1007/s13205-020-02384-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/07/2020] [Indexed: 10/23/2022] Open
Abstract
A biotin-labeled, non-isotopic, novel polyprobe was developed for the simultaneous detection of six viruses viz. apple chlorotic leaf spot virus (ACLSV), apple mosaic virus (ApMV), apple stem grooving virus (ASGV), cherry virus A (CVA), prunus necrotic ringspot virus (PNRSV) and plum pox virus (PPV) infecting stone and pome fruit trees through dot-blot hybridization assay. The sensitivity of the polyprobe was checked by serial dilutions of total RNA extracted from the tissues of infected trees. ACLSV was detected up to a dilution of 5-5, whereas ApMV, ASGV, CVA, PPV and PNRSV up to 5-4. The developed assay was validated following testing a total of 45 symptomatic leaf samples collected from different geographical regions of Jammu and Kashmir (India), and the presence of the viruses was further confirmed by RT-PCR and sequencing. The polyprobe, designed for performing molecular hybridization assay can be developed quickly and avoid the tedious transformation and cloning procedures. Apart from simultaneously detecting viruses in stone and pome fruit trees, it holds great potential for virus indexing programmes to ascertain the supply of virus-free plant materials to the growers.
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Affiliation(s)
- Md Salik Noorani
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard (A Deemed to be University), Hamdard Nagar, New Delhi, 110062 India.,Plant Virus Laboratory, Department of Biosciences, Jamia Millia Islamia (A Central University), Jamia Nagar, New Delhi, 110025 India
| | - Jawaid Ahmad Khan
- Plant Virus Laboratory, Department of Biosciences, Jamia Millia Islamia (A Central University), Jamia Nagar, New Delhi, 110025 India
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Jo Y, Choi H, Kim SM, Kim SL, Lee BC, Cho WK. Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus. BMC Genomics 2016; 17:579. [PMID: 27507588 PMCID: PMC4977635 DOI: 10.1186/s12864-016-2994-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/03/2016] [Indexed: 02/08/2023] Open
Abstract
Background Next-generation sequencing (NGS) provides many possibilities for plant virology research. In this study, we performed integrated analyses using plant transcriptome data for plant virus identification using Apple stem grooving virus (ASGV) as an exemplar virus. We used 15 publicly available transcriptome libraries from three different studies, two mRNA-Seq studies and a small RNA-Seq study. Results We de novo assembled nearly complete genomes of ASGV isolates Fuji and Cuiguan from apple and pear transcriptomes, respectively, and identified single nucleotide variations (SNVs) of ASGV within the transcriptomes. We demonstrated the application of NGS raw data to confirm viral infections in the plant transcriptomes. In addition, we compared the usability of two de novo assemblers, Trinity and Velvet, for virus identification and genome assembly. A phylogenetic tree revealed that ASGV and Citrus tatter leaf virus (CTLV) are the same virus, which was divided into two clades. Recombination analyses identified six recombination events from 21 viral genomes. Conclusions Taken together, our in silico analyses using NGS data provide a successful application of plant transcriptomes to reveal extensive information associated with viral genome assembly, SNVs, phylogenetic relationships, and genetic recombination. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2994-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yeonhwa Jo
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hoseong Choi
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Sang-Min Kim
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Sun-Lim Kim
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Bong Choon Lee
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Won Kyong Cho
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. .,The Taejin Genome Institute, Gadam-gil 61, Hoeongseong, 25239, Republic of Korea.
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Brakta A, Handa A, Thakur PD, Tomar M, Kumar P. Malus pumila 'Spy 227' and Apple stem pitting virus: graft incompatibility and epinasty. Virusdisease 2015; 26:92-6. [PMID: 26436128 DOI: 10.1007/s13337-014-0242-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 12/29/2014] [Indexed: 11/28/2022] Open
Abstract
Apple stem pitting foveavirus (ASPV) is one of the most important and widespread virus infecting apples in the world. Of late, the virus has been found to be invariably associated with most of the apple plantations of Shimla district of Himachal Pradesh based on DAS-ELISA results. Bioassay of viruses in vegetatively propagated crops including apple is considered to be an essential component in indexing programmes for the production of virus free propagating material. Woody indicator Malus pumila 'Spy 227' was used for the detection of ASPV through double grafting method. Graft incompatibility and epinasty symptoms were observed on Malus pumila Spy 227 indicator plants. Further, molecular identification of the virus isolate was done by cloning and sequencing of the test isolate. Partial sequence analysis of the coat protein gene showed 89 % nucleotide identity in BLASTN analysis with ASPV isolate from China (Accession No. JF895517). This is the first record of ASPV producing Graft incompatibility on Spy 227 indicator plants.
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Affiliation(s)
- Ajay Brakta
- Plant Virology Laboratory, Department of Plant Pathology, College of Horticulture, Dr. Y.S. Parmar University of Horticulture & Forestry, Nauni-Solan, 173230 HP India
| | - Anil Handa
- Plant Virology Laboratory, Department of Plant Pathology, College of Horticulture, Dr. Y.S. Parmar University of Horticulture & Forestry, Nauni-Solan, 173230 HP India
| | - P D Thakur
- Plant Virology Laboratory, Department of Plant Pathology, College of Horticulture, Dr. Y.S. Parmar University of Horticulture & Forestry, Nauni-Solan, 173230 HP India
| | - Manica Tomar
- Plant Virology Laboratory, Department of Plant Pathology, College of Horticulture, Dr. Y.S. Parmar University of Horticulture & Forestry, Nauni-Solan, 173230 HP India
| | - Pardeep Kumar
- Plant Virology Laboratory, Department of Plant Pathology, College of Horticulture, Dr. Y.S. Parmar University of Horticulture & Forestry, Nauni-Solan, 173230 HP India
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Arya P, Kumar G, Acharya V, Singh AK. Genome-wide identification and expression analysis of NBS-encoding genes in Malus x domestica and expansion of NBS genes family in Rosaceae. PLoS One 2014; 9:e107987. [PMID: 25232838 PMCID: PMC4169499 DOI: 10.1371/journal.pone.0107987] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 08/25/2014] [Indexed: 11/18/2022] Open
Abstract
Nucleotide binding site leucine-rich repeats (NBS-LRR) disease resistance proteins play an important role in plant defense against pathogen attack. A number of recent studies have been carried out to identify and characterize NBS-LRR gene families in many important plant species. In this study, we identified NBS-LRR gene family comprising of 1015 NBS-LRRs using highly stringent computational methods. These NBS-LRRs were characterized on the basis of conserved protein motifs, gene duplication events, chromosomal locations, phylogenetic relationships and digital gene expression analysis. Surprisingly, equal distribution of Toll/interleukin-1 receptor (TIR) and coiled coil (CC) (1 ∶ 1) was detected in apple while the unequal distribution was reported in majority of all other known plant genome studies. Prediction of gene duplication events intriguingly revealed that not only tandem duplication but also segmental duplication may equally be responsible for the expansion of the apple NBS-LRR gene family. Gene expression profiling using expressed sequence tags database of apple and quantitative real-time PCR (qRT-PCR) revealed the expression of these genes in wide range of tissues and disease conditions, respectively. Taken together, this study will provide a blueprint for future efforts towards improvement of disease resistance in apple.
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Affiliation(s)
- Preeti Arya
- Academy of Scientific & Innovative Research (AcSIR), New Dehli, India; Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Gulshan Kumar
- Academy of Scientific & Innovative Research (AcSIR), New Dehli, India; Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Vishal Acharya
- Academy of Scientific & Innovative Research (AcSIR), New Dehli, India; Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- * E-mail: (VA); (AKS)
| | - Anil K. Singh
- Academy of Scientific & Innovative Research (AcSIR), New Dehli, India; Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- * E-mail: (VA); (AKS)
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Kumar S, Singh L, Ram R, Zaidi AA, Hallan V. Simultaneous detection of major pome fruit viruses and a viroid. Indian J Microbiol 2014; 54:203-10. [PMID: 25320423 PMCID: PMC4188501 DOI: 10.1007/s12088-013-0431-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 10/13/2013] [Indexed: 11/29/2022] Open
Abstract
A rapid and sensitive two-step RT-PCR protocol for simultaneous detection of major apple viruses, namely Apple mosaic virus (ApMV), Apple stem pitting virus (ASPV), Apple stem grooving virus (ASGV), Apple chlorotic leaf spot virus (ACLSV) and Apple scar skin viroid (ASSVd), was developed. Five specific primer pairs were tested and confirmed for these viruses and viroid together in a single tube, giving amplicons of ~198, ~330, ~370, ~547 and ~645 bp corresponding to ASGV, ASSVd, ASPV, ApMV and ACLSV, respectively. Using a guanidinium-based extraction buffer along with a commercial kit resulted in better quality RNA as compared to kit, suited for multiplex RT-PCR. A rapid CTAB method for RNA isolation from apple tissue was developed, which produce good yield and saves time. To the best of our knowledge, this is the first report on the simultaneous detection of five pathogens (four viruses and a viroid) from apple with NADH dehydrogenase subunit 5 (nad5) as an internal control.
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Affiliation(s)
- Surender Kumar
- Plant Virology Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061 HP India
| | - Lakhmir Singh
- Plant Virology Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061 HP India
| | - Raja Ram
- Plant Virology Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061 HP India
| | - Aijaz A. Zaidi
- Plant Virology Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061 HP India
| | - Vipin Hallan
- Plant Virology Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061 HP India
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Molecular Detection of Latent Apple chlorotic leaf spot virus in Elite Mother Plants of Apple. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2012; 23:359-63. [PMID: 24293825 DOI: 10.1007/s13337-012-0117-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Accepted: 09/20/2012] [Indexed: 11/25/2022]
Abstract
Apple chlorotic leaf spot virus (ACLSV; family Betaflexiviridae genus Trichovirus) is one of the economically important latent virus infecting apple (Malus × domestica Borkh.). Reverse transcriptase polymerase chain reaction (RT-PCR) procedures were used to amplify coat protein gene of ACLSV. Among 5 primer sets used, two primer sets (1F1R and 1F2R) amplified fragments of expected size (432 bp). Products visible on agarose gel were produced using templates extracted from apple leaves. The results were further validated by sequencing fragment of 432 bp which was amplified from leaf of apple by using primer set 1F 1R. Comparisons with published sequences indicated that the isolate have very high 91 % identity values to the corresponding region of ACLSV isolate from apple. Selected primer pair (1F1R) was further used for screening 42 elite mother plants collected from apple growing areas of Himachal Pradesh, India, where in 17 were found free from ACLSV. Use of NAD5 gene in mitochondrial mRNA of the apple as an internal control, reduced the risk of false negative results that may occur with routine RT-PCR assays.
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